| Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae) | |
Wang, Fan-Hong1,2; Lu, Jin-Mei1 ; Wen, Jun3; Ebihara, Atsushi4; Li, De-Zhu1
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| 2016-09-07 | |
| Source Publication | PLOS ONE
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| Volume | 11Issue:9Pages:1 |
| Abstract | DNA barcoding is a fast-developing technique to identify species by using short and standard DNA sequences. Universal selection of DNA barcodes in ferns remains unresolved. In this study, five plastid regions (rbcL, matK, trnH-psbA, trnL-F and rps4-trnS) and eight nuclear regions (ITS, pgiC, gapC, LEAFY, ITS2, IBR3_2, DET1, and SQD1_1) were screened and evaluated in the fern genus Adiantum from China and neighboring areas. Due to low primer universality (matK) and/or the existence of multiple copies (ITS), the commonly used barcodes matK and ITS were not appropriate for Adiantum. The PCR amplification rate was extremely low in all nuclear genes except for IBR3_2. rbcL had the highest PCR amplification rate (94.33%) and sequencing success rate (90.78%), while trnH-psbA had the highest species identification rate (75%). With the consideration of discriminatory power, cost-efficiency and effort, the two-barcode combination of rbcL + trnH-psbA seems to be the best choice for barcoding Adiantum, and perhaps basal polypod ferns in general. The nuclear IBR3_2 showed 100% PCR amplification success rate in Adiantum, however, it seemed that only diploid species could acquire clean sequences without cloning. With cloning, IBR3_2 can successfully distinguish cryptic species and hybrid species from their related species. Because hybridization and allopolyploidy are common in ferns, we argue for including a selected group of nuclear loci as barcodes, especially via the next-generation sequencing, as it is much more efficient to obtain single-copy nuclear loci without the cloning procedure. |
| DOI | 10.1371/journal.pone.0160611 |
| Indexed By | SCI |
| Language | 英语 |
| WOS ID | WOS:000383255200005 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.kib.ac.cn/handle/151853/33615 |
| Collection | 中国西南野生生物种质资源库 |
| Affiliation | 1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China 2.Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China 3.Smithsonian Inst, Dept Bot, Natl Museum Nat Hist, Washington, DC 20560 USA 4.Natl Museum Nat & Sci, Dept Bot, Tsukuba, Ibaraki, Japan |
| Recommended Citation GB/T 7714 | Wang, Fan-Hong,Lu, Jin-Mei,Wen, Jun,et al. Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae)[J]. PLOS ONE,2016,11(9):1. |
| APA | Wang, Fan-Hong,Lu, Jin-Mei,Wen, Jun,Ebihara, Atsushi,&Li, De-Zhu.(2016).Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae).PLOS ONE,11(9),1. |
| MLA | Wang, Fan-Hong,et al."Applying DNA Barcodes to Identify Closely Related Species of Ferns: A Case Study of the Chinese Adiantum (Pteridaceae)".PLOS ONE 11.9(2016):1. |
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| pone.0160611.pdf（3648KB） | 期刊论文 | 作者接受稿 | 开放获取 | CC BY-NC-SA | View Download | |
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